BioC 3.4: CHECK report for ontoCAT on malbec1

Package: ontoCAT

Version: 1.26.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.26.0.tar.gz

StartedAt: 2017-04-15 00:14:34 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 00:16:37 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 122.8 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ontoCAT.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ontoCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ontoCAT’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ontoCAT’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
Ontology-class          96.264  1.040  35.911
showHierarchyDownToTerm  8.356  0.036   6.707
getEFO                   7.584  0.040   5.983
getAllTerms              5.144  0.024   3.485
searchTerm               5.052  0.004   3.053
getRootIds               5.008  0.012   3.450
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/ontoCAT.Rcheck/00check.log’
for details.

* installing *source* package ‘ontoCAT’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ontoCAT)

name	user	system	elapsed
Ontology-class	96.264	1.040	35.911
OntologyTerm-class	0.008	0.000	0.009
getAccession	0.004	0.000	0.005
getAllTermChildren	0.012	0.000	0.012
getAllTermIds	3.692	0.020	1.616
getAllTermParents	0.024	0.000	0.022
getAllTerms	5.144	0.024	3.485
getEFO	7.584	0.040	5.983
getEFOBranchRootIds	4.844	0.000	3.797
getLabel	0.008	0.000	0.005
getOntology	3.504	0.004	1.805
getOntologyAccession	0.004	0.000	0.003
getOntologyDescription	0.000	0.004	0.002
getRootIds	5.008	0.012	3.450
getRoots	3.708	0.020	2.945
getTermAndAllChildren	0.012	0.004	0.015
getTermById	0.008	0.000	0.006
getTermChildren	0.012	0.000	0.013
getTermDefinitions	0.012	0.000	0.012
getTermNameById	0.004	0.000	0.003
getTermParents	0.012	0.000	0.013
getTermSynonyms	0.024	0.004	0.029
hasTerm	0.004	0.000	0.004
isEFOBranchRoot	0.004	0.000	0.006
isRoot	3.648	0.020	2.927
ontoCAT-package	0.152	0.000	0.061
searchTerm	5.052	0.004	3.053
searchTermPrefix	3.576	0.008	2.983
showHierarchyDownToTerm	8.356	0.036	6.707
showPathsToTerm	3.844	0.024	3.100